My apologies- having never written a pymol script in my life,
it never occurred to me that your "cd" was a pymol command.
All my examples were from the DOS shell.

Still it may be helpful that the DOS 8.3 (Progra~1) names work.
You can get the short name of your directory by DIR/x
(from the dos shell) in the directory above.

David A. Horita wrote:
> Thanks for the replies/suggestions.  Looks like I may need to upgrade from 
> v1.1, but:
>
> cd \"program files", "\program files", and \program?files give a variant of
>
> PyMOL>cd \"program files"
> Traceback (most recent call last):
>    File "C:\Program Files\DeLano 
> Scientific\PyMOL/modules\pymol\externing.py", line 46, in cd
>      os.chdir(dir)  # raises on error
> OSError: [Errno 22] Invalid argument: '\\"program files"'
>
>
> cd \progra~1 does work, however.
> Pymol 1.1r1 running on Vista (32-bit) Business.
>
> -David
>
> -----Original Message-----
> From: Edward A. Berry [mailto:[email protected]]
> Sent: Mon 9/20/2010 2:03 PM
> Cc: [email protected]
> Subject: Re: [PyMOL] cd in windows
>
> David A. Horita wrote:
>> Hi,
>> How does one change directories in Windows when the directory name has a
>> space in it? I've tried double and single quotes as well as backslash
>> space (I'd like to run a script that's in such a directory).
>> Thanks
>> David
>
> These all work for me:
>   >cd \"program files"
>
>   >cd "\program files"
>
>   >cd \program?files
>
>   >dir/x \prog*
> 06/05/2010  10:02p<DIR>           PROGRA~1
>   >cd \progra~1
>
> Or run in your data directory using full path of the executable:
>   >\"program files"\seamonkey\seamonkey.exe
>
> (seamonkey is artemia the brine shrimp, you understand.
> Diminutive alternative to thunderbird and firefox)
>
> ------------------------------------------------------------------------------
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>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
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